ENST00000761288.1:n.238+9992G>A

Variant names:

• chr17-6249814-G-A
• rs3888640
• ENST00000761288.1:n.238+9992G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000761288.1(ENSG00000299154):​n.238+9992G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,058 control chromosomes in the GnomAD database, including 12,531 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (12531 hom., cov: 32)
• Consequence: ENSG00000299154 ENST00000761288.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 4 publications found

Genes affected

ENSG00000299154 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299154	ENST00000761288.1	n.238+9992G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60306 AN: 151938 Hom.: 12531 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.406

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.397 AC: 60328 AN: 152058 Hom.: 12531 Cov.: 32 AF XY: 0.398 AC XY: 29560 AN XY: 74308

African (AFR) AF: 0.317 AC: 13144 AN: 41476

American (AMR) AF: 0.400 AC: 6111 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3471 AN: 5160

South Asian (SAS) AF: 0.458 AC: 2202 AN: 4812

European-Finnish (FIN) AF: 0.419 AC: 4422 AN: 10562

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28175 AN: 67986

Other (OTH) AF: 0.409 AC: 863 AN: 2108

Alfa AF: 0.412 Hom.: 58355

Bravo AF: 0.393

Asia WGS AF: 0.571 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.64
PhyloP100		-0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3888640; hg19: chr17-6153134;